Sure, Kakashi is present in the Boruto manga. His role might not be as prominent as in the Naruto series, but he still has significant moments and interactions.
Kakashi is very much alive in the Boruto manga. The manga doesn't include his death. Maybe you got some misinformation or confused it with another character's fate. But for sure, Kakashi is around.
The plot could be that Naruto gets a special mission to protect Kakashi's face from a group of rogue ninjas who want to steal Kakashi's identity. Naruto has to use his unique skills to fend off the attackers and keep Kakashi's face safe.
A possible plotline could be that a new enemy targets Kakashi because of his distinct face features, believing there is some hidden power in his appearance. Naruto then has to protect Kakashi. Another plotline could be a magical spell that gets cast on Kakashi's face, changing his expressions uncontrollably, and Naruto tries to find a way to break the spell.
Some fanfictions might introduce new, original villains. For example, a dark sorcerer - type character who wants to use Naruto's unique chakra for his own evil purposes. Kakashi has to face this sorcerer and his minions to keep Naruto out of harm's way.
Well, for starters, Kakashi has to deal with Naruto's hyperactive and sometimes reckless behavior. Naruto often acts without thinking, which could put him in danger. Sasuke, with his complex emotions and the burden of his clan's massacre, is also a handful. Kakashi needs to make Sasuke understand that revenge is not the only way forward. Additionally, Kakashi has to ensure that both Naruto and Sasuke get along well with each other. There could be rivalry between them, and Kakashi has to manage that in a way that doesn't harm their relationship or their growth as ninjas.